Generated Code
The following is python code generated by the CellML API from this CellML file. (Back to language selection)
The raw code is available.
# Size of variable arrays:
sizeAlgebraic = 30
sizeStates = 8
sizeConstants = 81
from math import *
from numpy import *
def createLegends():
legend_states = [""] * sizeStates
legend_rates = [""] * sizeStates
legend_algebraic = [""] * sizeAlgebraic
legend_voi = ""
legend_constants = [""] * sizeConstants
legend_voi = "time in component environment (minute)"
legend_states[0] = "PYR in component PYR (millimolar)"
legend_algebraic[4] = "V_GLYC in component V_GLYC (flux)"
legend_algebraic[6] = "V_LDH in component V_LDH (flux)"
legend_algebraic[8] = "V_PDH in component V_PDH (flux)"
legend_algebraic[20] = "V_ALS in component V_ALS (flux)"
legend_states[1] = "ACP in component ACP (millimolar)"
legend_algebraic[10] = "V_PTA in component V_PTA (flux)"
legend_algebraic[14] = "V_ACK in component V_ACK (flux)"
legend_states[2] = "ACAL in component ACAL (millimolar)"
legend_algebraic[13] = "V_ACALDH in component V_ACALDH (flux)"
legend_algebraic[17] = "V_ADH in component V_ADH (flux)"
legend_states[3] = "ACLAC in component ACLAC (millimolar)"
legend_algebraic[22] = "V_ALDC in component V_ALDC (flux)"
legend_algebraic[27] = "V_NEALC in component V_NEALC (flux)"
legend_states[4] = "ACET in component ACET (millimolar)"
legend_algebraic[26] = "V_ACETDH in component V_ACETDH (flux)"
legend_algebraic[24] = "V_ACETEFF in component V_ACETEFF (flux)"
legend_states[5] = "ATP in component ATP (millimolar)"
legend_algebraic[18] = "V_ATPase in component V_ATPase (flux)"
legend_algebraic[0] = "ADP in component ADP (millimolar)"
legend_constants[0] = "A_tot in component ADP (millimolar)"
legend_states[6] = "NADH in component NADH (millimolar)"
legend_algebraic[29] = "V_NOX in component V_NOX (flux)"
legend_algebraic[1] = "NAD in component NAD (millimolar)"
legend_constants[1] = "NAD_tot in component NAD (millimolar)"
legend_states[7] = "ACCOA in component ACCOA (millimolar)"
legend_algebraic[2] = "COA in component COA (millimolar)"
legend_constants[2] = "C_tot in component COA (millimolar)"
legend_constants[3] = "AC in component AC (millimolar)"
legend_constants[4] = "BUT in component BUT (millimolar)"
legend_constants[5] = "ETOH in component ETOH (millimolar)"
legend_constants[6] = "GLC in component GLC (millimolar)"
legend_constants[7] = "LAC in component LAC (millimolar)"
legend_constants[8] = "O in component O (millimolar)"
legend_constants[9] = "P in component P (millimolar)"
legend_algebraic[3] = "V_GLYC_temp in component V_GLYC (flux)"
legend_constants[10] = "Km_GLC in component V_GLYC (millimolar)"
legend_constants[11] = "Km_NAD in component V_GLYC (millimolar)"
legend_constants[12] = "Km_ADP in component V_GLYC (millimolar)"
legend_constants[13] = "Km_PYR in component V_GLYC (millimolar)"
legend_constants[14] = "Km_NADH in component V_GLYC (millimolar)"
legend_constants[15] = "Km_ATP in component V_GLYC (millimolar)"
legend_constants[16] = "V_GLYC_max in component V_GLYC (flux)"
legend_algebraic[5] = "V_LDH_temp in component V_LDH (flux)"
legend_constants[17] = "Keq in component V_LDH (dimensionless)"
legend_constants[18] = "Km_LAC in component V_LDH (millimolar)"
legend_constants[19] = "Km_NAD in component V_LDH (millimolar)"
legend_constants[20] = "Km_PYR in component V_LDH (millimolar)"
legend_constants[21] = "Km_NADH in component V_LDH (millimolar)"
legend_constants[22] = "V_LDH_max in component V_LDH (flux)"
legend_algebraic[7] = "V_PDH_temp in component V_PDH (flux)"
legend_constants[23] = "Ki in component V_PDH (dimensionless)"
legend_constants[24] = "Km_NAD in component V_PDH (millimolar)"
legend_constants[25] = "Km_COA in component V_PDH (millimolar)"
legend_constants[26] = "Km_PYR in component V_PDH (millimolar)"
legend_constants[27] = "Km_NADH in component V_PDH (millimolar)"
legend_constants[28] = "Km_ACCOA in component V_PDH (millimolar)"
legend_constants[29] = "V_PDH_max in component V_PDH (flux)"
legend_algebraic[9] = "V_PTA_temp in component V_PTA (flux)"
legend_constants[30] = "Keq in component V_PTA (dimensionless)"
legend_constants[31] = "Km_P in component V_PTA (millimolar)"
legend_constants[32] = "Ki_P in component V_PTA (millimolar)"
legend_constants[33] = "Ki_COA in component V_PTA (millimolar)"
legend_constants[34] = "Km_ACP in component V_PTA (millimolar)"
legend_constants[35] = "Ki_ACP in component V_PTA (millimolar)"
legend_constants[36] = "Ki_ACCOA in component V_PTA (millimolar)"
legend_constants[37] = "V_PTA_max in component V_PTA (flux)"
legend_algebraic[12] = "V_ACK_temp in component V_ACK (flux)"
legend_constants[38] = "Keq in component V_ACK (dimensionless)"
legend_constants[39] = "Km_AC in component V_ACK (millimolar)"
legend_constants[40] = "Km_ATP in component V_ACK (millimolar)"
legend_constants[41] = "Km_ADP in component V_ACK (millimolar)"
legend_constants[42] = "Km_ACP in component V_ACK (millimolar)"
legend_constants[43] = "V_ACK_max in component V_ACK (flux)"
legend_algebraic[11] = "V_ACALDH_temp in component V_ACALDH (flux)"
legend_constants[44] = "Keq in component V_ACALDH (millimolar)"
legend_constants[45] = "Km_NAD in component V_ACALDH (millimolar)"
legend_constants[46] = "Km_NADH in component V_ACALDH (millimolar)"
legend_constants[47] = "Km_COA in component V_ACALDH (millimolar)"
legend_constants[48] = "Km_ACCOA in component V_ACALDH (millimolar)"
legend_constants[49] = "Km_ACAL in component V_ACALDH (millimolar)"
legend_constants[50] = "V_ACALDH_max in component V_ACALDH (flux)"
legend_algebraic[15] = "V_ADH_temp in component V_ADH (flux)"
legend_constants[51] = "Keq in component V_ADH (dimensionless)"
legend_constants[52] = "Km_NAD in component V_ADH (millimolar)"
legend_constants[53] = "Km_NADH in component V_ADH (millimolar)"
legend_constants[54] = "Km_ETOH in component V_ADH (millimolar)"
legend_constants[55] = "Km_ACAL in component V_ADH (millimolar)"
legend_constants[56] = "V_ADH_max in component V_ADH (flux)"
legend_algebraic[19] = "V_ALS_temp in component V_ALS (flux)"
legend_constants[57] = "N in component V_ALS (dimensionless)"
legend_constants[58] = "Keq in component V_ALS (dimensionless)"
legend_constants[59] = "Km_ACLAC in component V_ALS (millimolar)"
legend_constants[60] = "Km_PYR in component V_ALS (millimolar)"
legend_constants[61] = "V_ALS_max in component V_ALS (flux)"
legend_algebraic[21] = "V_ALDC_temp in component V_ALDC (flux)"
legend_constants[62] = "Km_ACLAC in component V_ALDC (millimolar)"
legend_constants[63] = "Km_ACET in component V_ALDC (millimolar)"
legend_constants[64] = "V_ALDC_max in component V_ALDC (flux)"
legend_algebraic[23] = "V_ACETEFF_temp in component V_ACETEFF (flux)"
legend_constants[65] = "Km_ACET in component V_ACETEFF (millimolar)"
legend_constants[66] = "V_ACETEFF_max in component V_ACETEFF (flux)"
legend_algebraic[25] = "V_ACETDH_temp in component V_ACETDH (flux)"
legend_constants[67] = "Keq in component V_ACETDH (dimensionless)"
legend_constants[68] = "Km_NAD in component V_ACETDH (millimolar)"
legend_constants[69] = "Km_NADH in component V_ACETDH (millimolar)"
legend_constants[70] = "Km_BUT in component V_ACETDH (millimolar)"
legend_constants[71] = "Km_ACET in component V_ACETDH (millimolar)"
legend_constants[72] = "V_ACETDH_max in component V_ACETDH (flux)"
legend_algebraic[16] = "V_ATPase_temp in component V_ATPase (flux)"
legend_constants[73] = "N in component V_ATPase (dimensionless)"
legend_constants[74] = "Km_ATP in component V_ATPase (dimensionless)"
legend_constants[75] = "V_ATPase_max in component V_ATPase (flux)"
legend_algebraic[28] = "V_NOX_temp in component V_NOX (flux)"
legend_constants[76] = "Km_NAD in component V_NOX (millimolar)"
legend_constants[77] = "Km_NADH in component V_NOX (millimolar)"
legend_constants[78] = "Km_O in component V_NOX (millimolar)"
legend_constants[79] = "V_NOX_max in component V_NOX (flux)"
legend_constants[80] = "k in component V_NEALC (first_order_rate_constant)"
legend_rates[0] = "d/dt PYR in component PYR (millimolar)"
legend_rates[1] = "d/dt ACP in component ACP (millimolar)"
legend_rates[2] = "d/dt ACAL in component ACAL (millimolar)"
legend_rates[3] = "d/dt ACLAC in component ACLAC (millimolar)"
legend_rates[4] = "d/dt ACET in component ACET (millimolar)"
legend_rates[5] = "d/dt ATP in component ATP (millimolar)"
legend_rates[6] = "d/dt NADH in component NADH (millimolar)"
legend_rates[7] = "d/dt ACCOA in component ACCOA (millimolar)"
return (legend_states, legend_algebraic, legend_voi, legend_constants)
def initConsts():
constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
states[0] = 1
states[1] = 0.03145
states[2] = 0.11
states[3] = 1e-5
states[4] = 1e-5
states[5] = 0.1
constants[0] = 5
states[6] = 3.67
constants[1] = 10
states[7] = 0.11
constants[2] = 1
constants[3] = 0.01
constants[4] = 0.01
constants[5] = 0.1
constants[6] = 15
constants[7] = 0.1
constants[8] = 0.2
constants[9] = 10
constants[10] = 0.1
constants[11] = 0.1412
constants[12] = 0.04699
constants[13] = 2.5
constants[14] = 0.08999
constants[15] = 0.01867
constants[16] = 2397
constants[17] = 21120.69
constants[18] = 100
constants[19] = 2.4
constants[20] = 1.5
constants[21] = 0.08
constants[22] = 5118
constants[23] = 46.4159
constants[24] = 0.4
constants[25] = 0.014
constants[26] = 1
constants[27] = 0.1
constants[28] = 0.008
constants[29] = 259
constants[30] = 0.0065
constants[31] = 2.6
constants[32] = 2.6
constants[33] = 0.029
constants[34] = 0.7
constants[35] = 0.2
constants[36] = 0.2
constants[37] = 42
constants[38] = 174.217
constants[39] = 7
constants[40] = 0.07
constants[41] = 0.5
constants[42] = 0.16
constants[43] = 2700
constants[44] = 1
constants[45] = 0.08
constants[46] = 0.025
constants[47] = 0.008
constants[48] = 0.007
constants[49] = 10
constants[50] = 97
constants[51] = 12354.9
constants[52] = 0.08
constants[53] = 0.05
constants[54] = 1
constants[55] = 0.03
constants[56] = 162
constants[57] = 2.4
constants[58] = 9e12
constants[59] = 100
constants[60] = 50
constants[61] = 600
constants[62] = 10
constants[63] = 100
constants[64] = 106
constants[65] = 5
constants[66] = 200
constants[67] = 1400
constants[68] = 0.16
constants[69] = 0.02
constants[70] = 2.6
constants[71] = 0.06
constants[72] = 105
constants[73] = 2.58
constants[74] = 6.196
constants[75] = 900
constants[76] = 1
constants[77] = 0.041
constants[78] = 0.2
constants[79] = 118
constants[80] = 0.0003
return (states, constants)
def computeRates(voi, states, constants):
rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
algebraic[2] = constants[2]-states[7]
algebraic[9] = ((constants[37]/(constants[36]*constants[31]))*(states[7]*constants[9]-(states[1]*algebraic[2])/constants[30]))/(1.00000+states[7]/constants[36]+constants[9]/constants[32]+states[1]/constants[35]+algebraic[2]/constants[33]+(states[7]*constants[9])/(constants[36]*constants[31])+(states[1]*algebraic[2])/(constants[34]*constants[33]))
algebraic[10] = custom_piecewise([greater_equal(algebraic[9] , 0.00000), algebraic[9] , True, algebraic[9]])
algebraic[0] = constants[0]-states[5]
algebraic[12] = ((constants[43]/(constants[41]*constants[42]))*(states[1]*algebraic[0]-(constants[3]*states[5])/constants[38]))/((1.00000+states[1]/constants[42]+constants[3]/constants[39])*(1.00000+algebraic[0]/constants[41]+states[5]/constants[40]))
algebraic[14] = custom_piecewise([greater_equal(algebraic[12] , 0.00000), algebraic[12] , True, algebraic[12]])
rates[1] = algebraic[10]-algebraic[14]
algebraic[1] = constants[1]-states[6]
algebraic[7] = (((((((constants[29]/(1.00000+(constants[23]*states[6])/algebraic[1]))*states[0])/constants[26])*algebraic[1])/constants[24])*algebraic[2])/constants[25])/((1.00000+states[0]/constants[26])*(1.00000+algebraic[1]/constants[24]+states[6]/constants[27])*(1.00000+algebraic[2]/constants[25]+states[7]/constants[28]))
algebraic[8] = custom_piecewise([greater_equal(algebraic[7] , 0.00000), algebraic[7] , True, algebraic[7]])
algebraic[11] = ((constants[50]/(constants[48]*constants[46]))*(states[7]*states[6]-(algebraic[1]*algebraic[2]*states[2])/constants[44]))/((1.00000+algebraic[1]/constants[45]+states[6]/constants[46])*(1.00000+states[7]/constants[48]+algebraic[2]/constants[47])*(1.00000+states[2]/constants[49]))
algebraic[13] = custom_piecewise([greater_equal(algebraic[11] , 0.00000), algebraic[11] , True, algebraic[11]])
rates[7] = algebraic[8]-(algebraic[13]+algebraic[10])
algebraic[15] = ((constants[56]/(constants[55]*constants[53]))*(states[2]*states[6]-(constants[5]*algebraic[1])/constants[51]))/((1.00000+algebraic[1]/constants[52]+states[6]/constants[53])*(1.00000+states[2]/constants[55]+constants[5]/constants[54]))
algebraic[17] = custom_piecewise([greater_equal(algebraic[15] , 0.00000), algebraic[15] , True, algebraic[15]])
rates[2] = algebraic[13]-algebraic[17]
algebraic[3] = ((((((constants[16]*constants[6])/constants[10])*algebraic[1])/constants[11])*algebraic[0])/constants[12])/((1.00000+constants[6]/constants[10]+states[0]/constants[13])*(1.00000+algebraic[1]/constants[11]+states[6]/constants[14])*(1.00000+algebraic[0]/constants[12]+states[5]/constants[15]))
algebraic[4] = custom_piecewise([greater_equal(algebraic[3] , 0.00000), algebraic[3] , True, algebraic[3]])
algebraic[16] = (constants[75]*(power(states[5]/algebraic[0], constants[73])))/(power(constants[74], constants[73])+power(states[5]/algebraic[0], constants[73]))
algebraic[18] = custom_piecewise([greater_equal(algebraic[16] , 0.00000), algebraic[16] , True, algebraic[16]])
rates[5] = (algebraic[4]+algebraic[14])-algebraic[18]
algebraic[5] = ((constants[22]/(constants[20]*constants[21]))*(states[0]*states[6]-(constants[7]*algebraic[1])/constants[17]))/((1.00000+states[0]/constants[20]+constants[7]/constants[18])*(1.00000+states[6]/constants[21]+algebraic[1]/constants[19]))
algebraic[6] = custom_piecewise([greater_equal(algebraic[5] , 0.00000), algebraic[5] , True, algebraic[5]])
algebraic[19] = (((constants[61]*states[0])/constants[60])*(1.00000-states[3]/(states[0]*constants[58]))*(power(states[0]/constants[60]+states[3]/constants[59], constants[57]-1.00000)))/(1.00000+power(states[0]/constants[60]+states[3]/constants[59], constants[57]))
algebraic[20] = custom_piecewise([greater_equal(algebraic[19] , 0.00000), algebraic[19] , True, algebraic[19]])
rates[0] = algebraic[4]-(algebraic[6]+algebraic[8]+algebraic[20])
algebraic[21] = ((constants[64]*states[3])/constants[62])/(1.00000+states[3]/constants[62]+states[4]/constants[63])
algebraic[22] = custom_piecewise([greater_equal(algebraic[21] , 0.00000), algebraic[21] , True, algebraic[21]])
algebraic[27] = constants[80]*states[3]
rates[3] = 0.500000*algebraic[20]-(algebraic[22]+algebraic[27])
algebraic[25] = ((constants[72]/(constants[71]*constants[69]))*(states[4]*states[6]-(constants[4]*algebraic[1])/constants[67]))/((1.00000+states[4]/constants[71]+constants[4]/constants[70])*(1.00000+states[6]/constants[69]+algebraic[1]/constants[68]))
algebraic[26] = custom_piecewise([greater_equal(algebraic[25] , 0.00000), algebraic[25] , True, algebraic[25]])
algebraic[23] = ((constants[66]*states[4])/constants[65])/(1.00000+states[4]/constants[65])
algebraic[24] = custom_piecewise([greater_equal(algebraic[23] , 0.00000), algebraic[23] , True, algebraic[23]])
rates[4] = (algebraic[22]+algebraic[27])-(algebraic[26]+algebraic[24])
algebraic[28] = ((constants[79]*states[6]*constants[8])/(constants[77]*constants[78]))/((1.00000+states[6]/constants[77]+algebraic[1]/constants[76])*(1.00000+constants[8]/constants[78]))
algebraic[29] = custom_piecewise([greater_equal(algebraic[28] , 0.00000), algebraic[28] , True, algebraic[28]])
rates[6] = (algebraic[4]+algebraic[8])-(algebraic[6]+algebraic[13]+algebraic[17]+algebraic[26]+algebraic[29])
return(rates)
def computeAlgebraic(constants, states, voi):
algebraic = array([[0.0] * len(voi)] * sizeAlgebraic)
states = array(states)
voi = array(voi)
algebraic[2] = constants[2]-states[7]
algebraic[9] = ((constants[37]/(constants[36]*constants[31]))*(states[7]*constants[9]-(states[1]*algebraic[2])/constants[30]))/(1.00000+states[7]/constants[36]+constants[9]/constants[32]+states[1]/constants[35]+algebraic[2]/constants[33]+(states[7]*constants[9])/(constants[36]*constants[31])+(states[1]*algebraic[2])/(constants[34]*constants[33]))
algebraic[10] = custom_piecewise([greater_equal(algebraic[9] , 0.00000), algebraic[9] , True, algebraic[9]])
algebraic[0] = constants[0]-states[5]
algebraic[12] = ((constants[43]/(constants[41]*constants[42]))*(states[1]*algebraic[0]-(constants[3]*states[5])/constants[38]))/((1.00000+states[1]/constants[42]+constants[3]/constants[39])*(1.00000+algebraic[0]/constants[41]+states[5]/constants[40]))
algebraic[14] = custom_piecewise([greater_equal(algebraic[12] , 0.00000), algebraic[12] , True, algebraic[12]])
algebraic[1] = constants[1]-states[6]
algebraic[7] = (((((((constants[29]/(1.00000+(constants[23]*states[6])/algebraic[1]))*states[0])/constants[26])*algebraic[1])/constants[24])*algebraic[2])/constants[25])/((1.00000+states[0]/constants[26])*(1.00000+algebraic[1]/constants[24]+states[6]/constants[27])*(1.00000+algebraic[2]/constants[25]+states[7]/constants[28]))
algebraic[8] = custom_piecewise([greater_equal(algebraic[7] , 0.00000), algebraic[7] , True, algebraic[7]])
algebraic[11] = ((constants[50]/(constants[48]*constants[46]))*(states[7]*states[6]-(algebraic[1]*algebraic[2]*states[2])/constants[44]))/((1.00000+algebraic[1]/constants[45]+states[6]/constants[46])*(1.00000+states[7]/constants[48]+algebraic[2]/constants[47])*(1.00000+states[2]/constants[49]))
algebraic[13] = custom_piecewise([greater_equal(algebraic[11] , 0.00000), algebraic[11] , True, algebraic[11]])
algebraic[15] = ((constants[56]/(constants[55]*constants[53]))*(states[2]*states[6]-(constants[5]*algebraic[1])/constants[51]))/((1.00000+algebraic[1]/constants[52]+states[6]/constants[53])*(1.00000+states[2]/constants[55]+constants[5]/constants[54]))
algebraic[17] = custom_piecewise([greater_equal(algebraic[15] , 0.00000), algebraic[15] , True, algebraic[15]])
algebraic[3] = ((((((constants[16]*constants[6])/constants[10])*algebraic[1])/constants[11])*algebraic[0])/constants[12])/((1.00000+constants[6]/constants[10]+states[0]/constants[13])*(1.00000+algebraic[1]/constants[11]+states[6]/constants[14])*(1.00000+algebraic[0]/constants[12]+states[5]/constants[15]))
algebraic[4] = custom_piecewise([greater_equal(algebraic[3] , 0.00000), algebraic[3] , True, algebraic[3]])
algebraic[16] = (constants[75]*(power(states[5]/algebraic[0], constants[73])))/(power(constants[74], constants[73])+power(states[5]/algebraic[0], constants[73]))
algebraic[18] = custom_piecewise([greater_equal(algebraic[16] , 0.00000), algebraic[16] , True, algebraic[16]])
algebraic[5] = ((constants[22]/(constants[20]*constants[21]))*(states[0]*states[6]-(constants[7]*algebraic[1])/constants[17]))/((1.00000+states[0]/constants[20]+constants[7]/constants[18])*(1.00000+states[6]/constants[21]+algebraic[1]/constants[19]))
algebraic[6] = custom_piecewise([greater_equal(algebraic[5] , 0.00000), algebraic[5] , True, algebraic[5]])
algebraic[19] = (((constants[61]*states[0])/constants[60])*(1.00000-states[3]/(states[0]*constants[58]))*(power(states[0]/constants[60]+states[3]/constants[59], constants[57]-1.00000)))/(1.00000+power(states[0]/constants[60]+states[3]/constants[59], constants[57]))
algebraic[20] = custom_piecewise([greater_equal(algebraic[19] , 0.00000), algebraic[19] , True, algebraic[19]])
algebraic[21] = ((constants[64]*states[3])/constants[62])/(1.00000+states[3]/constants[62]+states[4]/constants[63])
algebraic[22] = custom_piecewise([greater_equal(algebraic[21] , 0.00000), algebraic[21] , True, algebraic[21]])
algebraic[27] = constants[80]*states[3]
algebraic[25] = ((constants[72]/(constants[71]*constants[69]))*(states[4]*states[6]-(constants[4]*algebraic[1])/constants[67]))/((1.00000+states[4]/constants[71]+constants[4]/constants[70])*(1.00000+states[6]/constants[69]+algebraic[1]/constants[68]))
algebraic[26] = custom_piecewise([greater_equal(algebraic[25] , 0.00000), algebraic[25] , True, algebraic[25]])
algebraic[23] = ((constants[66]*states[4])/constants[65])/(1.00000+states[4]/constants[65])
algebraic[24] = custom_piecewise([greater_equal(algebraic[23] , 0.00000), algebraic[23] , True, algebraic[23]])
algebraic[28] = ((constants[79]*states[6]*constants[8])/(constants[77]*constants[78]))/((1.00000+states[6]/constants[77]+algebraic[1]/constants[76])*(1.00000+constants[8]/constants[78]))
algebraic[29] = custom_piecewise([greater_equal(algebraic[28] , 0.00000), algebraic[28] , True, algebraic[28]])
return algebraic
def custom_piecewise(cases):
"""Compute result of a piecewise function"""
return select(cases[0::2],cases[1::2])
def solve_model():
"""Solve model with ODE solver"""
from scipy.integrate import ode
# Initialise constants and state variables
(init_states, constants) = initConsts()
# Set timespan to solve over
voi = linspace(0, 10, 500)
# Construct ODE object to solve
r = ode(computeRates)
r.set_integrator('vode', method='bdf', atol=1e-06, rtol=1e-06, max_step=1)
r.set_initial_value(init_states, voi[0])
r.set_f_params(constants)
# Solve model
states = array([[0.0] * len(voi)] * sizeStates)
states[:,0] = init_states
for (i,t) in enumerate(voi[1:]):
if r.successful():
r.integrate(t)
states[:,i+1] = r.y
else:
break
# Compute algebraic variables
algebraic = computeAlgebraic(constants, states, voi)
return (voi, states, algebraic)
def plot_model(voi, states, algebraic):
"""Plot variables against variable of integration"""
import pylab
(legend_states, legend_algebraic, legend_voi, legend_constants) = createLegends()
pylab.figure(1)
pylab.plot(voi,vstack((states,algebraic)).T)
pylab.xlabel(legend_voi)
pylab.legend(legend_states + legend_algebraic, loc='best')
pylab.show()
if __name__ == "__main__":
(voi, states, algebraic) = solve_model()
plot_model(voi, states, algebraic)